PMC:7252096 / 88955-89743 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T1011","span":{"begin":31,"end":35},"obj":"Body_part"},{"id":"T1012","span":{"begin":36,"end":42},"obj":"Body_part"},{"id":"T1013","span":{"begin":53,"end":56},"obj":"Body_part"},{"id":"T1014","span":{"begin":608,"end":613},"obj":"Body_part"}],"attributes":[{"id":"A1011","pred":"fma_id","subj":"T1011","obj":"http://purl.org/sig/ont/fma/fma7195"},{"id":"A1012","pred":"fma_id","subj":"T1012","obj":"http://purl.org/sig/ont/fma/fma9637"},{"id":"A1013","pred":"fma_id","subj":"T1013","obj":"http://purl.org/sig/ont/fma/fma278683"},{"id":"A1014","pred":"fma_id","subj":"T1014","obj":"http://purl.org/sig/ont/fma/fma68646"}],"text":"Surgical samples from diseased lung tissue (n = 3 TB+HIV+; n = 3 TB+; n = 2 non-infected patients) were processed as described in (Ardain et al., 2019). Briefly, each sample was collected into cold RP-10 (RPMI (Sigma-Aldrich) + 10% FBS), minced, and incubated for 25-30 min at 37°C with digestion buffer containing collagenase D (Sigma-Aldrich), DNase I (Sigma-Aldrich) in RPMI 1640 (Sigma-Aldrich) with 10% FBS (Hyclone). Following incubation, samples were homogenized using a GentleMACS, filtered using a 70 μm metal strainer, and pelleted by centrifugation at 400 g for 5 min. After obtaining the pellet, cells were resuspended in RP-10, passed through another 70μm strainer (Corning), stained with trypan blue, and then counted and diluted for scRNA-seq using Seq-Well S3 (see below)."}

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T206","span":{"begin":31,"end":35},"obj":"Body_part"},{"id":"T207","span":{"begin":36,"end":42},"obj":"Body_part"}],"attributes":[{"id":"A206","pred":"uberon_id","subj":"T206","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A207","pred":"uberon_id","subj":"T207","obj":"http://purl.obolibrary.org/obo/UBERON_0000479"}],"text":"Surgical samples from diseased lung tissue (n = 3 TB+HIV+; n = 3 TB+; n = 2 non-infected patients) were processed as described in (Ardain et al., 2019). Briefly, each sample was collected into cold RP-10 (RPMI (Sigma-Aldrich) + 10% FBS), minced, and incubated for 25-30 min at 37°C with digestion buffer containing collagenase D (Sigma-Aldrich), DNase I (Sigma-Aldrich) in RPMI 1640 (Sigma-Aldrich) with 10% FBS (Hyclone). Following incubation, samples were homogenized using a GentleMACS, filtered using a 70 μm metal strainer, and pelleted by centrifugation at 400 g for 5 min. After obtaining the pellet, cells were resuspended in RP-10, passed through another 70μm strainer (Corning), stained with trypan blue, and then counted and diluted for scRNA-seq using Seq-Well S3 (see below)."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T355","span":{"begin":50,"end":52},"obj":"Disease"},{"id":"T356","span":{"begin":65,"end":67},"obj":"Disease"},{"id":"T357","span":{"begin":198,"end":203},"obj":"Disease"},{"id":"T358","span":{"begin":634,"end":639},"obj":"Disease"}],"attributes":[{"id":"A355","pred":"mondo_id","subj":"T355","obj":"http://purl.obolibrary.org/obo/MONDO_0018076"},{"id":"A356","pred":"mondo_id","subj":"T356","obj":"http://purl.obolibrary.org/obo/MONDO_0018076"},{"id":"A357","pred":"mondo_id","subj":"T357","obj":"http://purl.obolibrary.org/obo/MONDO_0008379"},{"id":"A358","pred":"mondo_id","subj":"T358","obj":"http://purl.obolibrary.org/obo/MONDO_0008379"}],"text":"Surgical samples from diseased lung tissue (n = 3 TB+HIV+; n = 3 TB+; n = 2 non-infected patients) were processed as described in (Ardain et al., 2019). Briefly, each sample was collected into cold RP-10 (RPMI (Sigma-Aldrich) + 10% FBS), minced, and incubated for 25-30 min at 37°C with digestion buffer containing collagenase D (Sigma-Aldrich), DNase I (Sigma-Aldrich) in RPMI 1640 (Sigma-Aldrich) with 10% FBS (Hyclone). Following incubation, samples were homogenized using a GentleMACS, filtered using a 70 μm metal strainer, and pelleted by centrifugation at 400 g for 5 min. After obtaining the pellet, cells were resuspended in RP-10, passed through another 70μm strainer (Corning), stained with trypan blue, and then counted and diluted for scRNA-seq using Seq-Well S3 (see below)."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T1486","span":{"begin":31,"end":35},"obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"T1487","span":{"begin":31,"end":35},"obj":"http://www.ebi.ac.uk/efo/EFO_0000934"},{"id":"T1488","span":{"begin":476,"end":477},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T1489","span":{"begin":505,"end":506},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T1490","span":{"begin":608,"end":613},"obj":"http://purl.obolibrary.org/obo/GO_0005623"}],"text":"Surgical samples from diseased lung tissue (n = 3 TB+HIV+; n = 3 TB+; n = 2 non-infected patients) were processed as described in (Ardain et al., 2019). Briefly, each sample was collected into cold RP-10 (RPMI (Sigma-Aldrich) + 10% FBS), minced, and incubated for 25-30 min at 37°C with digestion buffer containing collagenase D (Sigma-Aldrich), DNase I (Sigma-Aldrich) in RPMI 1640 (Sigma-Aldrich) with 10% FBS (Hyclone). Following incubation, samples were homogenized using a GentleMACS, filtered using a 70 μm metal strainer, and pelleted by centrifugation at 400 g for 5 min. After obtaining the pellet, cells were resuspended in RP-10, passed through another 70μm strainer (Corning), stained with trypan blue, and then counted and diluted for scRNA-seq using Seq-Well S3 (see below)."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T14251","span":{"begin":198,"end":200},"obj":"Chemical"},{"id":"T69462","span":{"begin":297,"end":303},"obj":"Chemical"},{"id":"T37713","span":{"begin":634,"end":636},"obj":"Chemical"},{"id":"T13716","span":{"begin":702,"end":713},"obj":"Chemical"},{"id":"T89927","span":{"begin":773,"end":775},"obj":"Chemical"}],"attributes":[{"id":"A52081","pred":"chebi_id","subj":"T14251","obj":"http://purl.obolibrary.org/obo/CHEBI_141419"},{"id":"A86098","pred":"chebi_id","subj":"T69462","obj":"http://purl.obolibrary.org/obo/CHEBI_35225"},{"id":"A36488","pred":"chebi_id","subj":"T37713","obj":"http://purl.obolibrary.org/obo/CHEBI_141419"},{"id":"A23284","pred":"chebi_id","subj":"T13716","obj":"http://purl.obolibrary.org/obo/CHEBI_78897"},{"id":"A51723","pred":"chebi_id","subj":"T89927","obj":"http://purl.obolibrary.org/obo/CHEBI_29388"}],"text":"Surgical samples from diseased lung tissue (n = 3 TB+HIV+; n = 3 TB+; n = 2 non-infected patients) were processed as described in (Ardain et al., 2019). Briefly, each sample was collected into cold RP-10 (RPMI (Sigma-Aldrich) + 10% FBS), minced, and incubated for 25-30 min at 37°C with digestion buffer containing collagenase D (Sigma-Aldrich), DNase I (Sigma-Aldrich) in RPMI 1640 (Sigma-Aldrich) with 10% FBS (Hyclone). Following incubation, samples were homogenized using a GentleMACS, filtered using a 70 μm metal strainer, and pelleted by centrifugation at 400 g for 5 min. After obtaining the pellet, cells were resuspended in RP-10, passed through another 70μm strainer (Corning), stained with trypan blue, and then counted and diluted for scRNA-seq using Seq-Well S3 (see below)."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T58","span":{"begin":287,"end":296},"obj":"http://purl.obolibrary.org/obo/GO_0007586"},{"id":"T59","span":{"begin":346,"end":353},"obj":"http://purl.obolibrary.org/obo/GO_0004530"}],"text":"Surgical samples from diseased lung tissue (n = 3 TB+HIV+; n = 3 TB+; n = 2 non-infected patients) were processed as described in (Ardain et al., 2019). Briefly, each sample was collected into cold RP-10 (RPMI (Sigma-Aldrich) + 10% FBS), minced, and incubated for 25-30 min at 37°C with digestion buffer containing collagenase D (Sigma-Aldrich), DNase I (Sigma-Aldrich) in RPMI 1640 (Sigma-Aldrich) with 10% FBS (Hyclone). Following incubation, samples were homogenized using a GentleMACS, filtered using a 70 μm metal strainer, and pelleted by centrifugation at 400 g for 5 min. After obtaining the pellet, cells were resuspended in RP-10, passed through another 70μm strainer (Corning), stained with trypan blue, and then counted and diluted for scRNA-seq using Seq-Well S3 (see below)."}

{"project":"LitCovid-sentences","denotations":[{"id":"T634","span":{"begin":0,"end":152},"obj":"Sentence"},{"id":"T635","span":{"begin":153,"end":422},"obj":"Sentence"},{"id":"T636","span":{"begin":423,"end":579},"obj":"Sentence"},{"id":"T637","span":{"begin":580,"end":788},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Surgical samples from diseased lung tissue (n = 3 TB+HIV+; n = 3 TB+; n = 2 non-infected patients) were processed as described in (Ardain et al., 2019). Briefly, each sample was collected into cold RP-10 (RPMI (Sigma-Aldrich) + 10% FBS), minced, and incubated for 25-30 min at 37°C with digestion buffer containing collagenase D (Sigma-Aldrich), DNase I (Sigma-Aldrich) in RPMI 1640 (Sigma-Aldrich) with 10% FBS (Hyclone). Following incubation, samples were homogenized using a GentleMACS, filtered using a 70 μm metal strainer, and pelleted by centrifugation at 400 g for 5 min. After obtaining the pellet, cells were resuspended in RP-10, passed through another 70μm strainer (Corning), stained with trypan blue, and then counted and diluted for scRNA-seq using Seq-Well S3 (see below)."}

{"project":"LitCovid-PubTator","denotations":[{"id":"2468","span":{"begin":198,"end":203},"obj":"Gene"},{"id":"2469","span":{"begin":634,"end":639},"obj":"Gene"},{"id":"2470","span":{"begin":89,"end":97},"obj":"Species"},{"id":"2471","span":{"begin":53,"end":56},"obj":"Species"},{"id":"2472","span":{"begin":702,"end":713},"obj":"Chemical"},{"id":"2473","span":{"begin":80,"end":88},"obj":"Disease"}],"attributes":[{"id":"A2468","pred":"tao:has_database_id","subj":"2468","obj":"Gene:3614"},{"id":"A2469","pred":"tao:has_database_id","subj":"2469","obj":"Gene:3614"},{"id":"A2470","pred":"tao:has_database_id","subj":"2470","obj":"Tax:9606"},{"id":"A2471","pred":"tao:has_database_id","subj":"2471","obj":"Tax:12721"},{"id":"A2472","pred":"tao:has_database_id","subj":"2472","obj":"MESH:D014343"},{"id":"A2473","pred":"tao:has_database_id","subj":"2473","obj":"MESH:D007239"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"Surgical samples from diseased lung tissue (n = 3 TB+HIV+; n = 3 TB+; n = 2 non-infected patients) were processed as described in (Ardain et al., 2019). Briefly, each sample was collected into cold RP-10 (RPMI (Sigma-Aldrich) + 10% FBS), minced, and incubated for 25-30 min at 37°C with digestion buffer containing collagenase D (Sigma-Aldrich), DNase I (Sigma-Aldrich) in RPMI 1640 (Sigma-Aldrich) with 10% FBS (Hyclone). Following incubation, samples were homogenized using a GentleMACS, filtered using a 70 μm metal strainer, and pelleted by centrifugation at 400 g for 5 min. After obtaining the pellet, cells were resuspended in RP-10, passed through another 70μm strainer (Corning), stained with trypan blue, and then counted and diluted for scRNA-seq using Seq-Well S3 (see below)."}

{"project":"2_test","denotations":[{"id":"32413319-31168092-20790568","span":{"begin":146,"end":150},"obj":"31168092"}],"text":"Surgical samples from diseased lung tissue (n = 3 TB+HIV+; n = 3 TB+; n = 2 non-infected patients) were processed as described in (Ardain et al., 2019). Briefly, each sample was collected into cold RP-10 (RPMI (Sigma-Aldrich) + 10% FBS), minced, and incubated for 25-30 min at 37°C with digestion buffer containing collagenase D (Sigma-Aldrich), DNase I (Sigma-Aldrich) in RPMI 1640 (Sigma-Aldrich) with 10% FBS (Hyclone). Following incubation, samples were homogenized using a GentleMACS, filtered using a 70 μm metal strainer, and pelleted by centrifugation at 400 g for 5 min. After obtaining the pellet, cells were resuspended in RP-10, passed through another 70μm strainer (Corning), stained with trypan blue, and then counted and diluted for scRNA-seq using Seq-Well S3 (see below)."}